PlotCHETAH: Plot the CHETAH classification on 2D visulization like t-SNE...

Description Usage Arguments Value Examples

View source: R/Utils_CHETAH.R

Description

Plot the CHETAH classification on 2D visulization like t-SNE + the corresponding classification tree, colored with the same colors

Usage

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PlotCHETAH(input, redD = NA, interm = FALSE, return = FALSE,
  tree = TRUE, pt.size = 1, return_col = FALSE, col = NULL)

Arguments

input

a SingleCellExperiment on which CHETAHclassifier has been run

redD

the name of the reducedDim of the input to use for plotting

interm

color the intermediate instead of the final types

return

return the plot instead of printing it

tree

plot the tree, along with the classification

pt.size

the point-size of the classication plot

return_col

whether the colors that are used for the classification plot should be returned

col

custom colors for the cell types. the colors should be named with the corresponding cell types

Value

a ggplot object

Examples

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## Standard plot (final types colored)
PlotCHETAH(input = input_mel)

## Intermediate types colored
PlotCHETAH(input = input_mel, interm = TRUE)

## Plot only the t-SNE plot
PlotCHETAH(input = input_mel, tree = FALSE)

CHETAH documentation built on Nov. 8, 2020, 8:02 p.m.